| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 3 I | 6 4 3 | 7 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 4 I | 16 4 8 | 17 3 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_38649.1_Instance_1 HL_38649.1,HL_3HHN_006,G1_C12 | G | G | AA | C | A | C | U | A | U | A | C | |||||||||||||||
| HL_38649.1_Sequence_1 HL_38649.13HHN_G1_C12 | G | G | AA | C | A | C | U | A | U | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_38649.1_Instance_2 HL_38649.1,HL_3IVK_001,G1_C12 | G | G | AA | C | A | C | U | A | U | A | C | |||||||||||||||
| HL_38649.1_Sequence_2 HL_38649.13IVK_G1_C12 | G | G | AA | C | A | C | U | A | U | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_38649.1_Instance_3 HL_38649.1,HL_2A64_006,C313_G324 | C | G | GC | G | C | A | U | G | C | A | G | |||||||||||||||
| HL_38649.1_Sequence_3 HL_38649.12A64_C313_G324 | C | G | GC | G | C | A | U | G | C | A | G | true | 76 | 0 | 0 | 4.00 | ||||||||||
| HL_38649.1_Instance_4 HL_38649.1,HL_7MLX_001,G11_C22 | G | U | GC | A | G | C | C | C | G | U | C | |||||||||||||||
| HL_38649.1_Sequence_4 HL_38649.17MLX_G11_C22 | G | U | GC | A | G | C | C | C | G | U | C | true | 69 | 0 | 0 | 5.11 | ||||||||||
| HL_38649.1_Instance_5 HL_38649.1,HL_4RMO_001,C11_G22 | C | U | GA | C | C | G | A | U | A | U | G | |||||||||||||||
| HL_38649.1_Sequence_5 HL_38649.14RMO_C11_G22 | C | U | GA | C | C | G | A | U | A | U | G | true | 77 | 0 | 0 | 3.86 |
1 2 s35 1 10 cWW 2 9 tSH 2 10 s55 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for HL_38649.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009378994,0.018460667,0.010720525,0.194585102,0.000000000],[0.017844226,0.009337380,0.218585035,0.013101324,0.000000000],[0.010696621,0.229254879,0.002029771,0.024718569,0.000000000],[0.194084748,0.013199104,0.024076884,0.009926171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G1 - C12 cWW BasepairNode | Deletion Probability [0.0000000006151445] | Pair Probability [[0.102679193,0.108699764,0.001232595,0.005809225,0.000000000],[0.103442026,0.108448060,0.001232595,0.001232595,0.000000000],[0.151830955,0.001232595,0.006025767,0.104618026,0.000000000],[0.114617401,0.107862583,0.001232595,0.079804024,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.009799118,0.979911808,0.009799118,0.000489956] | Left Letter Distribution [0.458333333,0.208333333,0.291666667,0.041666667,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair G2 - A11 tSH HairpinNode | Num Bases [6] | Left Index [3] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node C5:U10 Interaction | Interacting Bases [1,1] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C5 Interaction | Interacting Bases [2,2] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A6 Interaction | Interacting Bases [3,3] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C7 Interaction | Interacting Bases [4,4] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U8 Interaction | Interacting Bases [5,5] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A9 Interaction | Interacting Bases [6,6] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U10Sequences of instances from HL_38649.1:
> HL_38649.1 3HHN G 1 C 12 GGAACACUAUAC > HL_38649.1 3IVK G 1 C 12 GGAACACUAUAC > HL_38649.1 2A64 C 313 G 324 CGGCGCAUGCAG > HL_38649.1 7MLX G 11 C 22 GUGCAGCCCGUC > HL_38649.1 4RMO C 11 G 22 CUGACCGAUAUG